[ensembl-dev] Question Regarding VEP script warnings and --html option

[Mathias Lesche]

Hey Will,

thanks for the answers.

On 12/11/2013 01:02 PM, Will McLaren wrote:
> The first warning, ($data[4] is uninitialized), happens because the 5th
> column (the alternate allele, ALT) of your VCF line is not present -
> this usually means that there are fewer than 5 columns of data on that
> particular line, or the delimiter between the columns (space or tab) is
> not present or corrupted somehow.
>
> VEP expects at least the first 5 columns of the VCF (CHR, POS, ID, REF,
> ALT) to be populated or to have a null "." value - have a check of your
> VCF file to make sure that it looks OK. The vcftools package has a tool
> called vcf-validator which you can use to validate the format of VCF
> files, see http://vcftools.sourceforge.net/docs.html

You were absolutely right. The script complains about the last line 
which was an empty line. I removed it and it ran smoothly.

>
> Currently it's not possible to produce HTML (--html) and VCF (--vcf)
> output - to see the HTML output, remove --vcf from your command line. If
> you want the VCF output as well, you'd have to do that in a separate VEP
> run. If you intended to indicate that the input format was VCF, you
> should use "--format vcf".

Ah okay. I always ran both options and did not know that it is not 
possible. I ran them separately now and


Cheers
Mathias



>
> Regards
>
> Will McLaren
> Ensembl Variation
>
>
>
>
> On 11 December 2013 11:14, Mathias Lesche
> <mathias.lesche at biotec.tu-dresden.de
> <mailto:mathias.lesche at biotec.tu-dresden.de>> wrote:
>
>     Dear VEP developers,
>
>     I have two questions regarding the current VEP script (Version 74).
>
>     I call the script in the following way:
>     /opt/rocks/bin/perl
>     /projects/seq-work/user/all/__vep/vep-74/variant_effect___predictor.pl
>     <http://variant_effect_predictor.pl> -i input.vcf -o ouput.vcf
>     --species homo_sapiens --fork 6 --format vcf --cache --dir_cache
>     /projects/seq-work/user/all/__vep/vep-cache/ --sift p --polyphen p
>     --humdiv --total_length --numbers --protein --canonical --pubmed
>     --gmaf --maf_1kg --maf_esp --vcf --html --offline
>
>     When running the script I get the following warning:
>     Use of uninitialized value $data[4] in string eq at
>     /projects/seq-work/user/all/__vep/vep-74/Bio/EnsEMBL/__Variation/Utils/VEP.pm
>     line 415, <GEN0> line 837.
>     Use of uninitialized value $ref in length at
>     /projects/seq-work/user/all/__vep/vep-74/Bio/EnsEMBL/__Variation/Utils/VEP.pm
>     line 448, <GEN0> line 837.
>     Use of uninitialized value $alt in pattern match (m//) at
>     /projects/seq-work/user/all/__vep/vep-74/Bio/EnsEMBL/__Variation/Utils/VEP.pm
>     line 451, <GEN0> line 837.
>     Use of uninitialized value $alt in split at
>     /projects/seq-work/user/all/__vep/vep-74/Bio/EnsEMBL/__Variation/Utils/VEP.pm
>     line 540, <GEN0> line 837.
>     Use of uninitialized value $alt in pattern match (m//) at
>     /projects/seq-work/user/all/__vep/vep-74/Bio/EnsEMBL/__Variation/Utils/VEP.pm
>     line 549, <GEN0> line 837.
>     Use of uninitialized value $ref in concatenation (.) or string at
>     /projects/seq-work/user/all/__vep/vep-74/Bio/EnsEMBL/__Variation/Utils/VEP.pm
>     line 621, <GEN0> line 837.
>     Use of uninitialized value $alt in concatenation (.) or string at
>     /projects/seq-work/user/all/__vep/vep-74/Bio/EnsEMBL/__Variation/Utils/VEP.pm
>     line 621, <GEN0> line 837.
>     Use of uninitialized value $data[2] in string eq at
>     /projects/seq-work/user/all/__vep/vep-74/Bio/EnsEMBL/__Variation/Utils/VEP.pm
>     line 621, <GEN0> line 837.
>     Use of uninitialized value in pattern match (m//) at
>     /projects/seq-work/user/all/__vep/vep-74/Bio/EnsEMBL/__Variation/Utils/VEP.pm
>     line 2395, <GEN0> line 837.
>     Use of uninitialized value in substitution (s///) at
>     /projects/seq-work/user/all/__vep/vep-74/Bio/EnsEMBL/__Variation/Utils/VEP.pm
>     line 2395, <GEN0> line 837.
>     Use of uninitialized value in string eq at
>     /projects/seq-work/user/all/__vep/vep-74/Bio/EnsEMBL/__Variation/Utils/VEP.pm
>     line 2396, <GEN0> line 837.
>     Use of uninitialized value in pattern match (m//) at
>     /projects/seq-work/user/all/__vep/vep-74/Bio/EnsEMBL/__Variation/Utils/VEP.pm
>     line 2401, <GEN0> line 837.
>     Use of uninitialized value in concatenation (.) or string at
>     /projects/seq-work/user/all/__vep/vep-74/Bio/EnsEMBL/__Variation/Utils/VEP.pm
>     line 2402, <GEN0> line 837.
>
>     But the calculation of the variations finishes. I'm just wondering
>     if it comes from the vcf file or is from the script itself.
>
>     Secondly the output.vcf.html is empty. It doesn't show the variants
>     or any links to Ensembl. Is there a way to fix it? But I use the
>     --html option.
>
>     I have to say I don't run vep on the whole vcf file. It is only a
>     portion of it including the header.
>
>     Regards,
>     Mathias Lesche
>     --
>     Mathias Lesche, Dipl. Bioinformatician
>     Deep Sequencing Group - SFB655
>     c/o DFG-Center for Regenerative Therapies Dresden
>     Cluster of Excellence / TU Dresden
>     Fetscherstraße 105
>     01307 Dresden
>
>     Phone: +49 (351) 458 82362 <tel:%2B49%20%28351%29%20458%2082362>
>     Email: mathias.lesche(at)biotec.tu-__dresden.de
>     <http://biotec.tu-dresden.de>
>
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